Research workbench
F factor trai relaxase domain bound to F orit single-stranded DNA
Analyse F factor trai relaxase domain bound to F orit single-stranded DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A0I
- Type
- protein + DNA
- Length
- 303 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- F plasmid single-stranded orit DNA; Trai protein
- EC
- 3.6.1.-
- UniProt
- P14565
- Ligands
- MG
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | F plasmid single-stranded orit DNA | dna | 10 | — | — |
| A | Trai protein (EC 3.6.1.-) | protein | 293 | 44% helix, 16% strand | P14565 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.57 | 0.78 | 36 | empty |
| 2 | 88 | 0.36 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 1696 Ų buried · 51 hydrogen bonds · protein-nucleic
Compared structures
- 2A0I · F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA · the same entry in another collection · chain A against A, TM-score 1.00
- P14565 · AlphaFold monomer V2.0 prediction for multifunctional conjugation protein trai (P14565) · a predicted model of the same protein · chain A against A, TM-score 0.95
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P14565
- Elsewhere: RCSB PDB 2A0I · PDBe 2A0I · UniProt P14565
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